gfnff 0.3.0__tar.gz

gfnff-0.3.0/.editorconfig

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+# This file is part of gfnff.
+# SPDX-Identifier: LGPL-3.0-or-later
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{f90,F90,fh}]
+indent_style = space
+indent_size = 2
+max_line_length = 100
+
+[*.{c,h,cpp,hpp}]
+indent_style = space
+indent_size = 2
+
+[*.py]
+indent_style = space
+indent_size = 4
+max_line_length = 88
+
+[{meson.build,meson_options.txt,*.cmake,CMakeLists.txt}]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false

gfnff-0.3.0/.fprettify.rc

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+# This file is part of gfnff.
+# SPDX-Identifier: LGPL-3.0-or-later
+#
+# fprettify settings matching the style the sources already use:
+#   spaces around assignment and relational operators,
+#   none around arithmetic or logical ones (a*b+c, x.and.y),
+#   two-space indent, comments left alone.
+#
+# The sources carry !&< / !&> markers around blocks that must not be
+# reformatted (parameter tables, OpenMP clause lists). fprettify honours them.
+#
+#   fprettify -c .fprettify.rc src/**/*.f90
+#
+[fprettify]
+indent = 2
+line-length = 100
+
+# do not reflow existing continuation lines; the physics expressions are
+# broken by hand where the breaks carry meaning
+strict-indent = false
+enable-replacements = false
+c-relations = false
+
+whitespace-comma = false
+whitespace-assignment = true
+whitespace-decl = false
+whitespace-relational = true
+whitespace-logical = false
+whitespace-plusminus = false
+whitespace-multdiv = false
+whitespace-print = true
+whitespace-type = false
+whitespace-intrinsics = true
+
+# leave comment text and case alone; CLAUDE.md defines the comment styles and
+# a case pass would churn every line for no gain
+strip-comments = false
+disable-indent-mod = false

gfnff-0.3.0/.git-blame-ignore-revs

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+# Revisions to ignore in git blame (formatting-only changes).
+# git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# Formatting only: run fprettify with the checked-in config
+00a7ca018d0d1873166429793522d671e7d110fd

gfnff-0.3.0/.github/workflows/build-and-test.yml

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+name: Build and Test
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  # ── CMake ────────────────────────────────────────────────────────────────────
+  cmake:
+    name: CMake (gcc-${{ matrix.compiler_version }}, ${{ matrix.build_type }})
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        compiler_version: [12, 13]
+        build_type: [Debug, RelWithDebInfo]
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v5
+
+      - name: Install compilers and dependencies
+        run: |
+          sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+          sudo apt-get update
+          sudo apt-get install -y \
+            gcc-${{ matrix.compiler_version }} \
+            g++-${{ matrix.compiler_version }} \
+            gfortran-${{ matrix.compiler_version }} \
+            libopenblas-dev
+
+          echo "CC=gcc-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+          echo "CXX=g++-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+          echo "FC=gfortran-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+
+      - name: Configure with CMake
+        run: |
+          cmake -B build -S . \
+            -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+            -DCMAKE_C_COMPILER=${{ env.CC }} \
+            -DCMAKE_CXX_COMPILER=${{ env.CXX }} \
+            -DCMAKE_Fortran_COMPILER=${{ env.FC }}
+
+      - name: Build
+        run: cmake --build build --config ${{ matrix.build_type }}
+
+      - name: Test
+        run: |
+          ctest --test-dir build \
+                --output-on-failure \
+                -R '^gfnff/'
+
+  # ── Meson ────────────────────────────────────────────────────────────────────
+  meson:
+    name: Meson (gcc-${{ matrix.compiler_version }}, ${{ matrix.build_type }})
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        compiler_version: [12, 13]
+        build_type: [debug, debugoptimized]
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v5
+
+      - name: Install compilers and dependencies
+        run: |
+          sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+          sudo apt-get update
+          sudo apt-get install -y \
+            gcc-${{ matrix.compiler_version }} \
+            g++-${{ matrix.compiler_version }} \
+            gfortran-${{ matrix.compiler_version }} \
+            libopenblas-dev
+          pip install meson ninja
+
+          # CC/CXX/FC are picked up from the environment by Meson
+          echo "CC=gcc-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+          echo "CXX=g++-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+          echo "FC=gfortran-${{ matrix.compiler_version }}" >> $GITHUB_ENV
+
+      - name: Configure with Meson
+        run: |
+          meson setup build \
+            --buildtype=${{ matrix.build_type }} \
+            --warnlevel=0 \
+            -Dtests=true
+
+      - name: Build
+        run: ninja -C build
+
+      - name: Test
+        run: meson test -C build --print-errorlogs

gfnff-0.3.0/.github/workflows/docs.yml

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+# This file is part of gfnff.
+# SPDX-Identifier: LGPL-3.0-or-later
+#
+# Build the Sphinx documentation and deploy it to GitHub Pages.
+# The repository's Pages source must be set to "GitHub Actions".
+#
+# autodoc imports the package, which loads the compiled library, so the
+# package is built and installed first.
+
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install compiler and BLAS/LAPACK
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gfortran libopenblas-dev
+
+      - name: Install package and documentation dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[docs]'
+
+      - name: Build documentation
+        # -W: a warning (broken link, failed import) fails the build
+        run: make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    if: github.ref == 'refs/heads/master'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build-docs
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

gfnff-0.3.0/.github/workflows/wheels.yml

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+# This file is part of gfnff.
+# SPDX-Identifier: LGPL-3.0-or-later
+#
+# Build binary wheels and an sdist for PyPI.
+# Triggered on version tags (v*) or manually via workflow_dispatch.
+#
+# The cibuildwheel settings (interpreters, container setup, test command) live
+# in pyproject.toml under [tool.cibuildwheel], so a local cibuildwheel run
+# builds and tests exactly what this workflow does.
+#
+# Every wheel is installed into a clean environment and run against
+# python/tests before anything is uploaded; a test failure blocks the release.
+#
+# The bindings are pure ctypes, so there is one py3-none wheel per platform.
+#
+# Platform coverage:
+#   Linux  x86_64   : ubuntu-latest runner, manylinux_2_28
+#   Linux  aarch64  : ubuntu-24.04-arm runner (native, no QEMU)
+#   macOS  arm64    : macos-14 runner (Apple Silicon, Homebrew gfortran)
+#   Windows         : not yet supported (requires mingw-w64 gfortran in CI)
+#
+# OpenMP note:
+#   find_package(OpenMP) in CMakeLists.txt is intentionally non-fatal.
+#   On macOS, Apple Clang (C/CXX) has no native OpenMP; Homebrew gfortran
+#   does.  CMake detects OpenMP_Fortran_FOUND and enables it for Fortran only.
+#
+# Dependency bundling:
+#   Linux  : auditwheel repair (run automatically by cibuildwheel) bundles
+#            libgfortran.so and libgomp.so into the wheel.
+#   macOS  : delocate bundles Homebrew gfortran runtime dylibs.
+#
+# macOS runner pinned to macos-14:
+#   Homebrew compiles gcc dylibs against the host OS.  On macOS 15 (macos-latest)
+#   the dylibs carry minOS=15.0, which delocate-wheel rejects for a 14.0 wheel.
+#   macos-14 produces dylibs with minOS=14.0, matching MACOSX_DEPLOYMENT_TARGET.
+#
+# Linux aarch64 runner:
+#   QEMU emulation on x86_64 is 10-20x slower than native.  ubuntu-24.04-arm
+#   provides a native arm64 runner (free for public repos).
+
+name: Build wheels
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            archs: x86_64
+          - os: ubuntu-24.04-arm
+            archs: aarch64
+          - os: macos-14
+            archs: arm64
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install gfortran (macOS)
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          brew install gcc
+          # Homebrew installs gfortran as gfortran-NN; find the highest version
+          # and symlink it to a plain 'gfortran' name for CMake to discover.
+          GFORTRANS=$(ls "$(brew --prefix)"/bin/gfortran-[0-9]* 2>/dev/null || true)
+          if [ -z "$GFORTRANS" ]; then
+            echo "No gfortran-* binary found after brew install gcc" >&2; exit 1
+          fi
+          GFORTRAN_BIN=$(printf '%s\n' $GFORTRANS | sort -t- -k2,2n | tail -n1)
+          echo "Using Fortran compiler: $GFORTRAN_BIN"
+          ln -sf "$GFORTRAN_BIN" "$(brew --prefix)/bin/gfortran"
+
+      - name: Build and test wheels
+        uses: pypa/cibuildwheel@v4.3.0
+        env:
+          CIBW_ARCHS: ${{ matrix.archs }}
+
+      - name: Upload wheel artifacts
+        uses: actions/upload-artifact@v5
+        with:
+          name: dist-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  # ---------------------------------------------------------------------------
+  # Source distribution: built, then installed from the tarball and tested, so
+  # that `pip install --no-binary gfnff` is known to work before it is uploaded
+  # ---------------------------------------------------------------------------
+  build_sdist:
+    name: Build and test sdist
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install compiler and BLAS/LAPACK
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gfortran libopenblas-dev
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: Install from sdist and test
+        run: |
+          python -m venv venv
+          venv/bin/pip install "$(ls dist/*.tar.gz)[test]"
+          # run the tests from a copy, away from the source tree, so that
+          # `import gfnff` resolves to the installed package
+          mkdir sdist-test
+          cp -r --parents python/tests param sdist-test/
+          cd sdist-test
+          ../venv/bin/python -c "from gfnff._lib import toml_available; assert toml_available()"
+          ../venv/bin/pytest python/tests
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v5
+        with:
+          name: dist-sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  # ---------------------------------------------------------------------------
+  # Upload to TestPyPI on manual workflow_dispatch (any branch, no tag needed)
+  # ---------------------------------------------------------------------------
+  upload_testpypi:
+    name: Upload to TestPyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch'
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/gfnff
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: dist-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          # a dry run may be repeated for the same version
+          skip-existing: true
+
+  # ---------------------------------------------------------------------------
+  # Collect all wheels and the sdist and upload to PyPI on tagged releases
+  # ---------------------------------------------------------------------------
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gfnff
+    permissions:
+      id-token: write  # OIDC trusted publishing
+      contents: write  # needed to create a GitHub Release
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: dist-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+
+      - name: Create GitHub Release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release create ${{ github.ref_name }} dist/* --generate-notes --repo ${{ github.repository }}

gfnff-0.3.0/.gitignore

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+*.o
+*.mod
+*.a
+*.tgz
+*.old
+github_bin/
+build_majestix
+build_commands
+_build*/
+build*/
+src/gfn0
+bin/
+testprog/gfn0
+testprog/coord
+ff/
+*/.wraplock
+*.bak
+.*/
+!.git/
+!.github/
+gfnff_topo
+gfnff_adjacency
+__pycache__
+python/gfnff/libgfnff*
+*.egg-info/
+dist/
+
+# meson fetches toml-f on demand via subprojects/toml-f.wrap; unlike
+# test-drive it is not a submodule, because only the meson build uses it
+subprojects/toml-f/
+subprojects/test-drive.wrap
+
+# generated by test/tools/mkindex.py, kept local
+project_index.md
+
+# sphinx: autosummary stubs are regenerated on every build
+docs/generated/

gfnff-0.3.0/.gitmodules

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+[submodule "subprojects/test-drive"]
+	path = subprojects/test-drive
+	url = https://github.com/fortran-lang/test-drive.git